Rapid diagnostic test for LAMP
Kits and methods are described that are directed to specific and sensitive methods of target nucleic acid detection and more specifically detecting target nucleic acids directly from biological samples. The kits and methods were developed to be easy to use involving a minimum number of steps and giving rapid and consistent results either at point of care or in high throughput situations. The kits and methods utilize in various combinations, reversible inhibitors of kit components, thermolabile enzymes, poloxamers, various salts, indicators and one or more Loop-Mediated Isothermal Amplification (LAMP) primer sets for detecting single and/or multiple targets and variants of the targets including SARS-CoV-2 targets and variants thereof in a single reaction. The kits and methods permit detection of the target nucleic with similar sensitivity regardless of the presence of undefined mutations that may enhance the virulence of cells or viruses containing the undefined mutations.
1. A kit for use in diagnostic detection of a target nucleic acid and variants thereof having undefined mutations, obtained from a cell or virus in a biological sample, the kit comprising:
(a) a lyophilized mixture of a strand displacing polymerase and an indicator reagent and optionally a lyophilized reverse transcriptase, wherein:
(i) the indicator reagent is characterized by its ability to change color or provide fluorescence in a nucleic acid amplification reaction; and
(ii) the strand displacing polymerase when rehydrated is capable of amplifying DNA at a temperature in the range of 50° C.-68° C.;
(b) a universal primer set suitable for loop mediated amplification (LAMP) of the target nucleic acids and variants thereof containing undefined mutations within one or more of the primer binding sites;
wherein the universal primer set suitable for LAMP is capable of hybridizing to the target DNA in the presence of a plurality of undefined mutations, and is configured to provide a positive result for the target DNA in a predetermined assay time period otherwise determined for a positive sample of a target nucleic acid having a known sequence;
wherein any of the reagents in the kit may be combined in a mixture in a single container or provided in separate containers.
2. The kit according to claim 1 , wherein the universal primer set suitable for loop mediated amplification (LAMP) are similarly diagnostic for the target nucleic acids and variants thereof where the any deletions and additions in the BIF and FIP primer binding sites of the variants do not exceed 6-9 nucleotides.
3. The kit according to claim 1 , wherein the target DNA is the reverse transcription product of an RNA virus.
4. The kit according to claim 3 , wherein the RNA virus is a coronavirus.
5. The kit according to claim 1 , wherein the indicator reagent is a molecular beacon or a metallochromic dye.
6. The kit according to claim 1 , further comprising (c) a lysis reagent in a container for receiving the biological sample, wherein the lysis reagents comprise a reducing agent and a metal chelator.
7. The kit according to claim 6 , wherein the reducing agent is Tris (2-carboxyethyl) phosphine hydrochloride (TCEP).
8. The kit according to any of claim 1 , wherein the lysis reagents comprise at least one of a salt of C—(NH 2 ) 2 NH + and a poloxamer.
9. The kit according to claim 1 , wherein one or more of components in (a)-(b) are immobilized on a substrate.
10. The kit according to claim 1 , comprising the reverse transcriptase, wherein the reverse transcriptase is a virus encoded reverse transcriptase, or a bacteria encoded intron II reverse transcriptase.
11. A method for detecting a target nucleic acid or unknown variant thereof in a biological sample by Loop-Mediated Isothermal Amplification (LAMP), comprising:
(a) combining the biological sample with a lysis reagent to form a lysis mix;
(b) incubating the lysis mix at a temperature of at least 60° C. for a period of time in the range of 2 minutes to 45 minutes;
(c) combining in a reaction mix, an aliquot of the heat treated lysis mix of step (b) with amplification reagents comprising a strand displacing polymerase, a reversible inhibitor of the polymerase, nucleoside triphosphates, and at least one set of LAMP primers that is capable of hybridizing to the target nucleic acid and to undefined variants of the target nucleic acid; and
(d) incubating the reaction mix for a reaction positive period of time under amplification conditions for LAMP to detect the presence of the target nucleic acid or undefined variants thereof in the sample.
12. The method of claim 11 , wherein the lysis reagent comprises a reducing agent and a metal chelating reagent.
13. The method of claim 11 , wherein (b) further comprises incubating the lysis mix at 95° C. for 5 minutes.
14. The method of claim 11 , wherein the amplification reagents include a reverse transcriptase and a reversible inhibitor of the reverse transcriptase.
15. The method according to claim 11 , wherein any of the reagents in the lysis mix and any of the amplification reagents may be lyophilized prior to combining with the biological sample.
16. The method according to claim 11 , wherein any of the reagents in the lysis mix and any of the amplification reagents may be immobilized on a matrix.
17. The method according to claim 11 , wherein the biological sample is saliva.
18. The method according to claim 11 , wherein the target nucleic acid is an RNA virus.
19. The method according to claim 18 , wherein the RNA virus is a coronavirus and the amplification reagents include multiple sets of universal primers.
20. The method according to claim 11 , further comprising step (e) sequencing the detected target nucleic acid or variants thereof to determine the presence of a novel mutations.